[English] 日本語
Yorodumi
- PDB-5l4u: Crystal structure of FimH lectin domain in complex with 2-Fluoro-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l4u
TitleCrystal structure of FimH lectin domain in complex with 2-Fluoro-Heptylmannoside
ComponentsProtein FimH
KeywordsSUGAR BINDING PROTEIN / FimH / Type 1 pilus / urinary tract infection / UTI / carbohydrate / lectin / mannose / cell adhesion
Function / homology
Function and homology information


pilus tip / mechanosensory behavior / cell adhesion involved in single-species biofilm formation / pilus / cell-substrate adhesion / D-mannose binding / host cell membrane / cell adhesion
Similarity search - Function
FimH, mannose-binding domain / FimH, mannose binding / Fimbrial-type adhesion domain / Fimbrial-type adhesion domain / Fimbrial protein / : / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
heptyl 2-fluoro-alpha-D-mannopyranoside / Type 1 fimbrin D-mannose specific adhesin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJakob, R.P. / Zihlmann, P. / Rabbani, S. / Maier, T. / Ernst, B.
CitationJournal: To Be Published
Title: High-Affinity Carbohydrate-Lectin Interactions: How Nature Makes it Possible
Authors: Zihlmann, P. / Jiang, X. / Sager, C.P. / Fiege, B. / Jakob, R.P. / Siegrist, S. / Zalewski, A. / Rabbani, S. / Eris, D. / Silbermann, M. / Pang, L. / Muhlethaler, T. / Sharpe, T. / Maier, T. / Ernst, B.
History
DepositionMay 26, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein FimH
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3944
Polymers33,8342
Non-polymers5612
Water7,837435
1
A: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1972
Polymers16,9171
Non-polymers2801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein FimH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1972
Polymers16,9171
Non-polymers2801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.550, 68.300, 96.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein FimH


Mass: 16916.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fimH, b4320, JW4283 / Plasmid: pTRC99a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P08191
#2: Sugar ChemComp-6KS / heptyl 2-fluoro-alpha-D-mannopyranoside / 2-Fluoro-Heptylmannoside / heptyl 2-fluoro-alpha-D-mannoside / heptyl 2-fluoro-D-mannoside / heptyl 2-fluoro-mannoside


Type: D-saccharide / Mass: 280.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H25FO5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.2 M (NH4)2SO4, 0.1 M Hepes pH 7 and 25-30% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.1→55.65 Å / Num. obs: 24925 / % possible obs: 99.4 % / Redundancy: 6.4 % / Biso Wilson estimate: 29.19 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.9
Reflection shellResolution: 2.1→2.33 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 2.2 / % possible all: 99

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XO8

4xo8


Resolution: 2.1→55.65 Å / Cor.coef. Fo:Fc: 0.9371 / Cor.coef. Fo:Fc free: 0.9229 / SU R Cruickshank DPI: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.228 / SU Rfree Blow DPI: 0.179 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1222 4.9 %RANDOM
Rwork0.2039 ---
obs0.2055 24925 99.47 %-
Displacement parametersBiso mean: 30.53 Å2
Baniso -1Baniso -2Baniso -3
1--10.3522 Å20 Å20 Å2
2--2.6332 Å20 Å2
3---7.719 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: 1 / Resolution: 2.1→55.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2407 0 38 435 2880
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092562HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.113577HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d799SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes370HARMONIC5
X-RAY DIFFRACTIONt_it2562HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion14.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion349SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3047SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2402 131 4.75 %
Rwork0.2232 2629 -
all0.224 2760 -
obs--99.47 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31770.19130.30640.6975-0.37662.80990.02040.00510.0091-0.02410.0692-0.0015-0.06330.0045-0.08960.0550.00860.0103-0.062-0.003-0.0855-18.6325-5.9426.8684
20.38520.1417-0.46740.28540.44513.07820.0398-0.006-0.0118-0.02660.05750.0066-0.01860.0366-0.09730.04820.0097-0.0001-0.05880.0009-0.0764-44.8925.888913.8526
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more